Simulating the isotropic Raman spectra of O-H stretching mode in liquid H2O based on a machine learning potential: the influence of vibrational couplings.

In this study, we trained a deep potential (DP) for H2O, an accurate machine learning (ML) potential. We performed molecular dynamics (MD) simulations of liquid water using the DP model (or DeePMD simulations). Our results showed that the DP model exhibits DFT-level accuracy, and the DeePMD simulation is a promising approach for modeling the structural properties of liquid water. Based on the DeePMD simulation trajectories, we calculated the isotropic Raman spectra of the O-H stretching mode using the surface-specific velocity-velocity correlation function (ssVVCF), showing that the DeePMD/ssVVCF approach can correctly capture the bimodal characteristics of the experimental Raman spectra, with one peak located near 3400 cm-1 and the other near 3250 cm-1. The success of the DeePMD/ssVVCF approach should be credited to (1) the DFT-level accuracy of the DP model for H2O, (2) the ssVVCF formulation considering the coupling between vibrational modes, and (3) non-Condon effects. Furthermore, the DeePMD simulations revealed that the anharmonic interactions between the coupled water molecules in the first and second hydration shells should play an essential role in the strong mixing of the H-O-H bending mode and the O-H stretching mode, leading to the delocalization of the O-H stretching band. In particular, increasing the strength of hydrogen bonds would enhance the bend-stretch coupling, leading to the red-shifting of the O-H vibrational spectra and the increase in the intensity of the shoulder around 3250 cm-1.

Binding of synthetic nanobodies to the SARS-CoV-2 receptor-binding domain: the importance of salt bridges.

In this study, five different SARS-CoV-2 receptor-binding domain (RBD) models were created based on the crystal structures of RBD complexes with two synthetic nanobodies (Sb16 and Sb45). Microsecond all-atom MD simulations revealed that Sb16 and Sb45 substantially stabilized the flexible RBD loop (residues GLU471-SER494) due to the salt bridges and hydrogen bonding interactions between RBD and the synthetic nanobodies. However, the calculation of binding free energy displayed that Sb45 had a higher binding affinity to RBD than Sb16, in agreement with the experimental result. This is because Sb45 has stronger electrostatic attraction to RBD as compared to Sb16. In particular, the salt bridge GLU484-ARG33 in Sb45-RBD is stronger than the GLU484-LYS32 in Sb16-RBD. Furthermore, by comparing the binding affinity of Sb16 for two RBD mutants (E484K and K417N), we found that E484K mutation substantially reduced the binding affinity to Sb16, and K417N mutation had no significant effect, qualitatively in agreement with experimental studies. According to the binding free energy calculation, the strong electrostatic repulsion between LYS32 and LYS484 caused by E484K mutation destroys the salt bridge between LYS32 and GLU484 in the RBD wild type (WT). In contrast, the binding of the K417N mutant to Sb16 effectively maintains the salt bridge between LYS32 and GLU484. Therefore, our research suggests that the salt bridges between RBD and synthetic nanobodies are crucial for binding synthetic nanobodies to RBD, and a SARS-CoV-2 variant can escape neutralization from nanobodies by creating electrostatic repulsion between them.

Effect of Disulfide Bridge on the Binding of SARS-CoV-2 Fusion Peptide to Cell Membrane: A Coarse-Grained Study.

In this paper, we present the parameterization of the CAVS coarse-grained (CG) force field for 20 amino acids, and our CG simulations show that the CAVS force field could accurately predict the amino acid tendency of the secondary structure. Then, we used the CAVS force field to investigate the binding of a severe acute respiratory syndrome-associated coronavirus fusion peptide (SARS-CoV-2 FP) to a phospholipid bilayer: a long FP (FP-L) containing 40 amino acids and a short FP (FP-S) containing 26 amino acids. Our CAVS CG simulations displayed that the binding affinity of the FP-L to the bilayer is higher than that of the FP-S. We found that the FP-L interacted more strongly with membrane cholesterol than the FP-S, which should be attributed to the stable helical structure of the FP-L at the C-terminus. In addition, we discovered that the FP-S had one major and two minor membrane-bound states, in agreement with previous all-atom molecular dynamics (MD) studies. However, we found that both the C-terminal and N-terminal amino acid residues of the FP-L can strongly interact with the bilayer membrane. Furthermore, we found that the disulfide bond formed between Cys840 and Cys851 stabilized the helices of the FP-L at the C-terminus, enhancing the interaction between the FP-L and the bilayer membrane. Our work indicates that the stable helical structure is crucial for binding the SARS-CoV-2 FP to cell membranes. In particular, the helical stability of FP should have a significant influence on the FP-membrane binding.

An intramolecular-locked strategy for designing nonlinear optical materials with remarkable first hyperpolarizability.

To meet the expanding demands of high performance nonlinear optical (NLO) materials, an unprecedented intramolecular-locked strategy is proposed to design NLO materials with remarkable static first hyperpolarizability (ß0). This strategy means that importing a large steric hindrance group diphenylmethane (DPM) decreases the torsion angles (θ) between the donor {triphenylamine (TPA)} and acceptor {9-H-thioxanthen-9-one-10,10-dioxide (TXO)} units, as well as between the donor (TPA) and π-bridge (benzene) fragments. The decrease of θ can accelerate the intramolecular charge transfer and enhance the contributions of the TPA, TXO and quinoxaline-6,7-dicarbo-nitrile (QCN) fragments to the axial component of the ß0 value, and then the ß0 values of TPA-TXO (ß0 = 10 762 au) and TPA-QCN (ß0 = 22 495 au) are increased by 14.9% and 34.4%, respectively. Overall, the intramolecular-locked strategy is very effective for designing high performance NLO materials.

Effects of Fluorination and Molybdenum Codoping on Monoclinic BiVO4 Photocatalyst by HSE Calculations.

Monoclinic phase bismuth vanadate (BiVO4) is one of the most promising photoelectrochemical materials used in water-splitting photoelectrochemical cells. It could be even better if its band gap and charge transport characteristics were optimized. Although codoping of BiVO4 has proven to be an effective strategy, its effects are remarkably poorly understood. Using the Heyd-Scuseria-Ernzerhof (HSE) hybrid functional, we estimate the formation energy, electronic properties, and photocatalytic activities of F and Mo codoped BiVO4. We find that Mo atoms prefer to replace V atoms, whereas F atoms prefer to replace O atoms (FOMoV-doped BiVO4) under oxygen-poor conditions according to calculated formation energies. BiVO4 doped with FOMoV is found to be shallow-level doped, occurring with some continuum states above the conduction band edge, which is advantageous for photochemical catalysis. Moreover, FOMoV-doped BiVO4 shows absorption stronger than that of pure BiVO4 in the visible spectrum. Based on the band-edge calculation, BiVO4 doped with FOMoV still retains a high oxidizing capacity. It has been shown that FOMoV-doped BiVO4 exhibits a very high photocatalytic activity under visible light.

Different Binding Modes of SARS-CoV-1 and SARS-CoV-2 Fusion Peptides to Cell Membranes: The Influence of Peptide Helix Length.

Although the amino acid sequences of SARS-CoV-1 and SARS-CoV-2 fusion peptides (FPs) are highly conserved, the cryo-electron microscopy structures of the SARS-CoV-1 and SARS-CoV-2 spike proteins show that the helix length of SARS-CoV-1 FP is longer than that of SARS-CoV-2 FP. In this work, we simulated the membrane-binding models of SARS-CoV-1 and SARS-CoV-2 FPs and compared the binding modes of the FPs with the POPC/POPE/cholesterol bilayer membrane. Our simulation results show that the SARS-CoV-2 FP binds to the bilayer membrane more effectively than the SARS-CoV-1 FP. It is seen that the short N-terminal helix of SARS-CoV-2 FP is more favorable to insert into the target membrane than the long N-terminal helix of SARS-CoV-1 FP. Meanwhile, the potential of mean force calculations showed that the SARS-CoV-2 FP would prefer only one binding mode (N-terminal binding), whereas the SARS-CoV-1 FP has two favorable membrane-binding modes (C-terminal and N-terminal binding modes). Moreover, in the case of SARS-CoV-1 FP binding to the target membrane, the transition between the two binding modes is relatively fast. Finally, we discovered that the membrane-binding mode would influence the helix length of SARS-CoV-1 FP, while the helix length of SARS-CoV-2 FP could be stably maintained in the membrane-bound configurations. This work suggests that the short helix might endow the FP with high membrane-anchoring strength. In particular, the membrane-penetrating residues (Phe, Ile, and Leu) of short α-helix interact with the cell membrane more strongly than those of long α-helix.

Second-Order Nonlinear Optics Response of the Boron-Dipyrromethenes-Based Mislinked Expanded Porphyrins: Revealing the Role of the -BF2 Group.

Here, the mislinked expanded porphyrins singly (labeled A) and doubly (labeled B) neo-confused [22]smaragdyrin, the boron-dipyrromethenes-based mislinked expanded porphyrins singly (labeled C) and doubly (labeled D) neo-confused [22]smaragdyrin, where both C and D include a -BF2 group, are chosen to serve as the study objects, and theoretical calculations are carried out to study the role of the -BF2 group in the second-order nonlinear optics (NLO) behaviors. Results highlighted that the -BF2 group plays an important role for the second-order behaviors in mislinked expanded porphyrins; namely, embedding the -BF2 group well enhanced the hyper-Rayleigh scattering (HRS) value {ßHRS(0;0,0)}, C{ßHRS(0;0,0)}A{ßHRS(0;0,0)} = 2.0 and D{ßHRS(0;0,0)}B{ßHRS(0;0,0)} = 2.9, main owning to the fact that installing -BF2 increases the electron delocalization degree and decreases the excited energy of the crucial excited state.

Extension of the CAVS model to the simulation of helical peptides in a membrane environment.

Considering the effect of peptide insertion on the dipole potential of the lipid membrane, we extend the CAVS coarse-grained (CG) model to the simulation of helical peptides in a membrane environment. In this approach, the CG scheme for a peptide backbone is similar to the treatment in the united-atom model, while we treated the side chain of an amino acid by grouping 1-3 heavy atoms into a CG unit. The CAVS CG force field for peptides is optimized by reproducing the experimental results for the backbone (φ, ψ) distribution and predicting the PMF profiles of transferring organic molecules in a lipid bilayer membrane obtained from all-atom simulations. The CAVS simulation of a helical peptide in a phosphatidylcholine (PC) lipid bilayer revealed that the insertion of a peptide increases the dipole potential of the PC lipid bilayer, in which the peptide and its neutralized ions make a significant contribution. Finally, we carried out the CAVS simulation for five different helical peptides in the PC lipid bilayer to explore the behavior of peptide tilt, showing excellent agreement with the all-atom simulations. Our work suggests that the peptide tilt should relieve the deformation stress from the lipid bilayer, and the peptide aggregation could reduce the peptide tilt by resisting the deformation stress from the surrounding lipids.

Electronic Spin Moment As a Catalytic Descriptor for Fe Single-Atom Catalysts Supported on C2N.

The electrocatalytic activity of transition-metal-based compounds is strongly related to the spin states. However, the underlying relationship connecting spin to catalytic activity remains unclear. Herein, we carried out density functional theory calculations on oxygen reduction reaction (ORR) catalyzed by Fe single-atom supported on C2N (C2N-Fe) to shed light on this relationship. It is found that the change of electronic spin moments of Fe and O2 due to molecular-catalyst adsorption scales with the amount of electron transfer from Fe to O2, which promotes the catalytic activity of C2N-Fe for driving ORR. The nearly linear relationship between the catalytic activity and spin moment variation suggests electronic spin moment as a promising catalytic descriptor for Fe single-atom based catalysts. Following the revealed relationship, the ORR barrier on C2N-Fe was tuned to be as low as 0.10 eV through judicious manipulation of spin states. These findings thus provide important insights into the relationship between catalytic activity and spin, leading to new strategies for designing transition metal single-atom catalysts.

Adsorption of Organic Molecules and Surfactants on Graphene: A Coarse-Grained Study.

The research studies on the adsorption of surfactants on graphene help us to know how to use surfactants to exfoliate graphene from graphite or functionalize the graphene surface. Among them, molecular dynamics (MD) simulation has been widely used to investigate the adsorption of organic molecules and surfactants on graphene. In particular, coarse-grained (CG) MD simulation greatly improves the computational efficiency by simplifying the complexity of the studied systems, allowing us to explore the structure and dynamics of complex systems on larger spatial scales and longer time scales. However, an accurate prediction of the adsorption of surfactants on graphene is required by optimizing the interaction between surfactants and graphene, which is often overlooked by some CG models. In this work, we found that an accurate prediction of the adsorption enthalpies of organic molecules on graphene can be achieved by optimizing the interactions between organic molecules and benzene. Meanwhile, we simulated the adsorption of a surfactant on single-layer and double-layer graphene nanosheets, respectively. Our results revealed that increasing the temperature would favor the interactions between hydrophilic groups of surfactants. In addition, we discovered that the surfactant prefers to be adsorbed on the inner surfaces of double-layer graphene compared with the outer surfaces, and this is owing to the dehydration in the middle of double-layer graphene, which is beneficial to the hydrophilic interactions between surfactant molecules inside the double-layer graphene.

Hybrid Density Functional Theory Study of Native Defects and Nonmetal (C, N, S, and P) Doping in a Bi2WO6 Photocatalyst.

Native defects and nonmetal doping have been shown to be an effective way to optimize the photocatalytic properties of Bi2WO6. However, a detailed understanding of defect physics in Bi2WO6 has been lacking. Here, using the Heyd-Scuseria-Ernzerhof hybrid functional defect calculations, we study the formation energies, electronic structures, and optical properties of native defects and nonmetal element (C, N, S, and P) doping into Bi2WO6. We find that the Bi vacancy (Bivac), O vacancy (Ovac), S doping on the O site (SO), and N doping on the O site (NO) defects in the Bi2WO6 can be stable depending on the Fermi level and chemical potentials. By contrast, the substitution of an O atom by a C or P atom (CO, PO) has high formation energy and is unlikely to form. The calculated electronic structures of the Bivac, Ovac, SO, and NO defects indicate that the band-gap reduction of Ovac 2+, Bivac 3-, and SO defects is mainly due to forming shallow impurity levels within the band gap. The calculated absorption coefficients of Ovac 2+, Bivac 3-, and SO show strong absorption in the visible light region, which is in good agreement with the experimental results. Hence, Ovac 2+, Bivac 3-, and SO defects can improve the adsorption capacity of Bi2WO6, which helps enhance its photocatalytic performance. Our results provide insights into how to enhance the photocatalytic activity of Bi2WO6 for energy and environmental applications through the rational design of defect-controlled synthesis conditions.

Effects of native defects and cerium impurity on the monoclinic BiVO4 photocatalyst obtained via PBE+U calculations.

In this article, we report a periodic density functional theory (DFT) investigation on the formation of the native defects and cerium doping in monoclinic BiVO4 (m-BiVO4) and their effect on the electronic structures, using the Perdew-Burke-Ernzerhof functionals corrected for on-site Coulombic interactions (PBE+U). From the point defect formation energies and transition levels, the Bivac (Bi vacancy), Vvac (V vacancy), Oint (O interstitial) and CeV (Ce doping on V site) defects in m-BiVO4 are identified as shallow acceptors. For Ce doping in m-BiVO4, the substitution of Bi by Ce is energetically favorable in the single positively charged state (Ce) under Bi/V-poor conditions, while the substitution of V by Ce is in the single negatively charged state (Ce) under O-rich conditions. The calculated electronic structures suggest that Ce degrades the activity by an unoccupied deep level in the gap region, mainly composed of Ce 4f orbitals, which makes this defect as the photogenerated electron-hole recombination center, in good agreement with the experimental results. For Ce, no localized state exists within the calculated band gap. Its formation energy is sensitive to the chemical potentials and Fermi energy, suggesting that the Bi/V-poor and O-rich conditions are desirable to eliminate the deep-level states and improve photocatalysis. Our results provide insights into enhancing the photocatalytic activity of m-BiVO4 for energy and environmental applications through the rational design of defect-controlled synthesis conditions.

Interfacial Water Structure at Zwitterionic Membrane/Water Interface: The Importance of Interactions between Water and Lipid Carbonyl Groups.

In this work, atomistic molecular dynamics (MD) simulations of palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer were carried out to investigate the effect of water models on membrane dipole potential, which is primarily associated with the preferential orientation of molecular dipoles at the membrane-water interface. We discovered that the overestimation of the dipole potential by the TIPS3P water model can be effectively reduced by the TIP4P water model. On the one hand, the TIP4P water model decreases the negative contribution of lipid to the dipole potential through influencing the orientation of lipid headgroups. On the other hand, the TIP4P water model reduces the positive contribution of water to the dipole potential by increasing the preference of H-down orientation (the water dipole orients toward the bilayer center). Interestingly, the TIP4P water model affects the orientation of interfacial water molecules more obviously than that of lipid headgroups, leading to the decrease in the dipole potential. Furthermore, the MD results revealed that the water close to the positively charged choline (namely, N-associated water) prefers the H-down orientation while the water around the negatively charged phosphate (namely, P-associated water) favors the H-up orientation, in support of recent experimental and MD studies. However, interfacial water molecules are more strongly influenced by the phosphate groups than by the choline groups, resulting in the net H-up orientation (the water dipole orients toward the bilayer center) in the region of lipid headgroups. In addition, it is intriguing that the preference of H-up orientation decreases when water molecules penetrate more deeply into the lipid bilayer. This is attributed to the counteracting effect of lipid carbonyl groups, and the effect varies with the lipid chains (oleoyl and palmitoyl chains), suggesting the important role of lipid carbonyl groups.

Atom-Pair Catalysts Supported by N-Doped Graphene for the Nitrogen Reduction Reaction: d-Band Center-Based Descriptor.

Achieving an effective nitrogen reduction reaction (NRR) under mild conditions is a great challenge for industrial ammonia synthesis. NRR is often accompanied by a competing hydrogen evolution reaction (HER), which causes an extremely low Faraday efficiency. We systematically investigated the NRR reactivity of atom-pair catalysts (APCs) formed by 20 transition metal (TM) elements supported by N-doped graphene via three reaction pathways. By analyzing the correlation among the limiting potential, Gibbs free energy, and d-band center, we evaluated the activity trends of the TM APCs. Our computations revealed that the enzymatic pathway is the most suitable reaction pathway for the TM APCs, and the intrinsic activity trend of these APCs can be determined by the d-band center-based descriptor, which has a simple linear correlation with the bonding/antibonding orbital population. In addition, the NRR APCs with excellent performance have been screened out through selective analysis of the competing HER in the electrocatalytic NRR process.

An ultra-effective pathway for fully removing the oxygen components of graphene oxide by a flame-assisted microwave process.

Here we report an ultra-effective and reliable pathway to reduce GO into graphene by an about 4 seconds flame-assisted microwave process. A holey graphene with a C/O atom ratio of 31.1, a pore volume of 6.0 cm3 g-1, and a specific surface area of 1050.0 m2 g-1 was synthesized.

An intermittent microwave-exfoliated non-expansive graphite oxide process for highly-efficient production of high-quality graphene.

Redox methods represented by Hummers' method are the most frequently-used pathways to prepare graphene, but to date still very low-efficient, because of its time-consuming washing and hard reduction process. Here we report an intermittent microwave-exfoliated non-expansive graphite oxide (GtO) process to prepare a wrinkled graphene with a high reduction degree (C/O: 19.0), a high defect degree, and a high specific surface area (1333.7 m2 g-1). Findings show that the non-expansive GtO without water washing indicates an almost 100% exfoliated success rate during this intermittent microwave process. The obtained graphene shows easy dispersity in organic solvents, and excellent supercapacitor performance in specific capacitance, rate capacity, and especially in cycling lifetime with no decay after 80,000 cycles at 30 A g-1. Consequently, this special microwave process successfully solves the problems of tedious washing and hard reduction in redox methods, thus exponentially boosting the efficiency of preparing graphene.

Effects of Ether Linkage on Membrane Dipole Potential and Cholesterol Flip-Flop Motion in Lipid Bilayer Membranes.

In our previous work, we investigated the effect of ether linkage on the physical properties of lipid bilayers using all-atom (AA) simulations with different water models. However, the influence of ether linkage on the transportation of cholesterol in lipid bilayers is less well studied. In order to reduce computational costs in simulations at large time and length scales, we present coarse-grained (CG) simulations of diphytanyl phosphatidylcholine (ether-DPhPC) and diphytanoyl phosphatidylcholine (ester-DPhPC) bilayer membranes in this work. First, the CG and AA simulations consistently show that the substitution of ether linkage for ester linkage would prevent the penetration of water into the lipid bilayer membranes. Second, it is encouraging that the CG simulations can nicely capture the ether effect on membrane dipole potential, showing that the ether substitution for ester would significantly decrease the dipole potential. In particular, the CG results agree with the AA simulation results, revealing that the change in the dipole potential is accompanied with the alteration in the orientation of linkage group. Finally, we carried out 60 µs CG simulations of ether-DPhPC and ester-DPhPC bilayers at two cholesterol concentrations (10 and 40% mole fraction, respectively), showing that the ether substitution for ester would facilitate the cholesterol flip-flop motion in lipid bilayer membranes.

Effect of Cholesterol and 6-Ketocholestanol on Membrane Dipole Potential and Sterol Flip-Flop Motion in Bilayer Membranes.

A variety of experimental and theoretical approaches have been employed to investigate the sterol flip-flop motion in lipid bilayer membranes. However, the sterol effect on the dipole potential of lipid bilayer membranes is less well studied and the influence of dipole potential on sterol flip-flop motion in lipid bilayer membranes is less well understood. In our previous works, we have demonstrated the performance of our coarse-grained (CG) model in the computation of the dipole potential. In this work, five 30 µs CG simulations of dimyristoylphosphatidylcholine (DMPC) bilayers were carried out at different sterol concentrations (in a range from 10 to 50% mole fraction). Then, a comparison was made between the effects of cholesterol (CHOL) and 6-ketocholestanol (6-KC) on the dipole potential of DMPC lipid bilayers as well as the sterol flip-flop motion. Our CG simulations show that the membrane dipole potential is impacted more significantly by 6-KC than by CHOL. This finding is consistent with recent experimental studies. Meanwhile, our work suggests that the sterol-sterol interactions (in particular, electrostatic interactions) should be critical to the formation of sterol-sterol clusters, which would hinder the sterol flip-flop motion inside the lipid bilayers. This is in support of the recent experimental study on the sterol transportation in lipid bilayer membranes.

Comparative study of the binding mode between cytochrome P450 17A1 and prostate cancer drugs in the absence of haem iron.

According to the X-ray crystal structures of CYP17A1 (including its complexes with inhibitors), it is shown that a hydrogen bond exists between CYP17A1 and its inhibitors (such as abiraterone and TOK-001). Previous short MD simulations (50 ns) suggested that the binding of abiraterone to CYP17A1 is stronger than that of TOK-001. In this work, by carrying out long atomistic MD simulations (200 ns) of CYP17A1 and its complexes with abiraterone and TOK-001, we observed a binding mode between CYP17A1 and abiraterone, which is different from the binding mode between CYP17A1 and TOK-001. In the case of abiraterone binding, the unfilled volume in the active site cavity increases the freedom of movement of abiraterone within CYP17A1, leading to the collective motions of the helices G and B' as well as the breaking of hydrogen bond existing between the 3ß-OH group of abiraterone and N202 of CYP17A1. However, the unfilled volume in the active site cavity can be occupied by the benzimidazole ring of TOK-001, restraining the motion of TOK-001. By pulling the two inhibitors (abiraterone and TOK-001) out of the binding pocket in CYP17A1, we discovered that abiraterone and TOK-001 were moved from their binding sites to the surface of protein similarly through the channels formed by the helices G and B'. In addition, based on the free energy calculations, one can see that it is energetically favorable for the two inhibitors (abiraterone and TOK-001) to enter into the binding pocket in CYP17A1.

Molecular Dynamics Simulations of Ether- and Ester-Linked Phospholipid Bilayers: A Comparative Study of Water Models.

Membrane dipole potential influences a variety of important biological processes involving cell membranes. Because it is quite challenging to directly measure the membrane dipole potential in experiments, molecular dynamics (MD) simulation has emerged as a powerful tool for a reasonable prediction of the dipole potential. Although MD predictions agree well with experiments about the sign of the dipole potential, the magnitude of the dipole potential varies significantly with the force field parameters. It has been shown that the positive dipole potential of phosphatidylcholine (PC) bilayer membranes would be overestimated by a nonpolarizable model owing to the treatment of many-body polarization effects in a mean-field fashion. In this work, we carried out atomistic MD simulations of the diphytanyl PC (ether-DPhPC) and diphytanoyl PC (ester-DPhPC) bilayers and made a comparative study of three different nonpolarizable water models (TIP3P, TIP4P, and TIP5P). Interestingly, we discover that the calculated dipole potential by the TIP5P model shows good agreement with the result obtained using the cryoelectron microscopy experiment, suggesting that a better description of electrostatic interactions in a nonpolarizable water model can effectively ameliorate the overestimation in the calculation of the dipole potential. In addition, our MD results show that the substitution of the ether linkage for the ester linkage of phospholipid bilayers would bring about a change in the orientation of the linkage group with respect to the bilayer normal, leading to the difference in the membrane dipole potential. Surprisingly, although water molecules provide a major contribution to the positive dipole potential, they have a limited impact on the difference of the dipole potential between the ether-DPhPC and ester-DPhPC bilayer membranes.